Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / broadinstitute/picard issues and pull requests
#1729 - Read CIGAR M operator maps off end of reference
Issue -
State: closed - Opened by BaylieRW almost 3 years ago
- 1 comment
#1725 - [Documentation] Could the main README list the supported java version ranges, that work with picard?
Issue -
State: closed - Opened by rubyFeedback about 3 years ago
- 2 comments
#1724 - GtcToVcf & CreateExtendedIlluminaManifest - support for GRCh38
Issue -
State: open - Opened by kew24 about 3 years ago
- 4 comments
#1721 - Update CrosscheckFingerprints summary
Pull Request -
State: closed - Opened by derekca about 3 years ago
- 3 comments
#1720 - Feature request: common flag to disable metrics requiring external dependencies (e.g. R)
Issue -
State: open - Opened by matthdsm about 3 years ago
- 3 comments
Labels: R-Dependency
#1710 - MergeBamAlignment needlessly requires input BAMs to be sorted by queryname
Issue -
State: closed - Opened by freeseek about 3 years ago
- 7 comments
#1709 - Picard from Bionconda 2.26 can not read BARCODE_FILE
Issue -
State: closed - Opened by crossz about 3 years ago
- 4 comments
#1693 - bug report: MergeBamAlignment fails to merge ubam and bam
Issue -
State: closed - Opened by fardokhtsadat over 3 years ago
- 2 comments
#1692 - Can't find picard-tools-x.y.z.zip at Latest Release project page.
Issue -
State: closed - Opened by rsharris over 3 years ago
- 4 comments
#1691 - BedToIntervalList error
Issue -
State: closed - Opened by xiucz over 3 years ago
- 2 comments
#1689 - Aligned record iterator (...) is behind the unmapped reads
Issue -
State: closed - Opened by marctormo over 3 years ago
- 3 comments
#1681 - Picard FixVcfHeader possible bug
Issue -
State: closed - Opened by NTNguyen13 over 3 years ago
- 1 comment
#1661 - ValidateSamFile diverges from SAM/BAM specification for read-group PL attribute
Issue -
State: closed - Opened by MikkelSchubert over 3 years ago
- 1 comment
#1657 - How you can keep RX barcode in uBAM after FastqToSam?
Issue -
State: closed - Opened by MatteoZam over 3 years ago
- 1 comment
#1652 - Markduplicates with UMI in GATK pipeline, which is the correct approach?
Issue -
State: open - Opened by MatteoZam over 3 years ago
- 3 comments
#1644 - installation instructions for picard version 1.43
Issue -
State: closed - Opened by JamalEH over 3 years ago
#1632 - How can I use CollectRnaSeqMetrics with an ENSEMBL annotated BAM file?
Issue -
State: closed - Opened by rpauly over 3 years ago
- 1 comment
#1631 - CollectVariantCallingMetrics throws NullPointerException
Issue -
State: closed - Opened by jezkoski over 3 years ago
- 2 comments
#1620 - Allow CollectRnaSeqMetrics to take in a GTF file
Pull Request -
State: closed - Opened by sophiacrennan almost 4 years ago
- 2 comments
Labels: On Hold
#1605 - CollectHsMetrics BAIT_INTERVALS and TARGET_INTERVALS need better definitions
Issue -
State: open - Opened by alanhoyle almost 4 years ago
- 1 comment
#1604 - getting error in MarkDuplicates
Issue -
State: closed - Opened by shanmugavadivelps almost 4 years ago
- 2 comments
#1588 - Add usage instructions to dockerhub
Issue -
State: open - Opened by moldach almost 4 years ago
- 1 comment
#1580 - Include common (engine-level) args in help output by default.
Pull Request -
State: closed - Opened by cmnbroad about 4 years ago
- 6 comments
#1565 - Error on fixing ReadGroups
Issue -
State: closed - Opened by elbakrifz about 4 years ago
- 1 comment
#1552 - LiftoverVCF does not liftover INFO/END for SVs
Issue -
State: open - Opened by cmnbroad about 4 years ago
- 12 comments
#1552 - LiftoverVCF does not liftover INFO/END for SVs
Issue -
State: open - Opened by cmnbroad about 4 years ago
- 9 comments
#1549 - Identify Contaminant Background Option and LoH handling
Pull Request -
State: closed - Opened by kachulis about 4 years ago
- 3 comments
Labels: On Hold
#1524 - Long references (>2^29)
Issue -
State: open - Opened by SergejN over 4 years ago
- 4 comments
#1496 - Bugfix for IdentifyContamiant + small improvements to Fingerprinting
Pull Request -
State: closed - Opened by yfarjoun over 4 years ago
- 4 comments
#1478 - Add the EXT argument to CollectSamErrorMetrics.
Pull Request -
State: closed - Opened by nh13 over 4 years ago
Labels: Waiting For Revisions
#1476 - Make the VCF option in CollectSamErrorMetrics optional.
Pull Request -
State: closed - Opened by nh13 over 4 years ago
Labels: Waiting For Revisions
#1474 - #Error:Heap-Memory Issues
Issue -
State: closed - Opened by Rohit-Satyam over 4 years ago
- 3 comments
#1473 - Intensity Test Data (BCL) Origin
Issue -
State: closed - Opened by emretaylanduman over 4 years ago
#1472 - BuildBamIndex should support index creation for CRAM
Issue -
State: open - Opened by cmnbroad over 4 years ago
#1462 - Bug Report: MergeBamAlignment Error: "String tag does not have length() == 2: Cross-species contamination | CO"
Issue -
State: closed - Opened by bhanugandham over 4 years ago
- 5 comments
#1459 - UmiAwareMarkDuplicatesWithMateCigar random error
Issue -
State: closed - Opened by sybrohee over 4 years ago
- 19 comments
#1452 - Liftover Issue for HGDP panel
Issue -
State: closed - Opened by Anahit19 over 4 years ago
- 1 comment
#1441 - MarkDuplicates Missing Optical Duplicates
Issue -
State: open - Opened by whitwham almost 5 years ago
- 7 comments
#1433 - Stop removing periods from the end of output names
Pull Request -
State: closed - Opened by tlangs almost 5 years ago
- 4 comments
#1431 - CollectInsertSizeMetrics Error
Issue -
State: closed - Opened by nicolasalexandre21 almost 5 years ago
- 2 comments
#1418 - liftover failed to recognize the swapped alleles
Issue -
State: closed - Opened by chenwenan almost 5 years ago
- 6 comments
#1416 - Encountered a contig, chr1_gl000192_random that is not part of the target reference
Issue -
State: closed - Opened by jefferyUstc almost 5 years ago
- 4 comments
#1409 - CollectWgsMetrics per chromosome merge
Issue -
State: closed - Opened by Stikus almost 5 years ago
- 3 comments
#1408 - Number of sequences in text header (34216887) != number of sequences in binary header (182084669)
Issue -
State: closed - Opened by shimingtan almost 5 years ago
- 2 comments
#1360 - Picard 2.20.3 markduplicates error
Issue -
State: closed - Opened by willright28 about 5 years ago
- 7 comments
#1355 - MarkDuplicates Code
Issue -
State: closed - Opened by fxjonas about 5 years ago
#1352 - MarkDuplicates CRAM output support?
Issue -
State: closed - Opened by simoncchu over 5 years ago
- 3 comments
#1340 - Update CollectSamErrorMetrics.java
Pull Request -
State: closed - Opened by nh13 over 5 years ago
- 6 comments
Labels: Waiting For Revisions
#1340 - Update CollectSamErrorMetrics.java
Pull Request -
State: closed - Opened by nh13 over 5 years ago
- 6 comments
Labels: Waiting For Revisions
#1330 - Meaning of CollectRnaSeqMetrics histogram?
Issue -
State: open - Opened by nicolerg over 5 years ago
- 4 comments
Labels: docs
#1276 - add R as a pre-requisite
Issue -
State: open - Opened by igordot over 5 years ago
Labels: R-Dependency
#1253 - queryname sorted BAM Markduplication ran a long time without any output
Issue -
State: closed - Opened by biozzq almost 6 years ago
- 4 comments
#1252 - pixel distance for MarkDuplicates Novaseq flow-cells
Issue -
State: closed - Opened by splaisan almost 6 years ago
- 6 comments
#1227 - IlluminaBasecallsToFastq does not write unassigned reads to file
Issue -
State: closed - Opened by rithy8 about 6 years ago
- 1 comment
#1194 - [bug] MarkDuplicates throws unexpected IllegalArgumentException with queryname-sorted input
Issue -
State: open - Opened by RWilton about 6 years ago
- 12 comments
#1159 - Error in MergeBamAlignment
Issue -
State: closed - Opened by alrafaykhan over 6 years ago
- 5 comments
#1081 - How to use USE_SEQUENTIAL_FASTQS option
Issue -
State: closed - Opened by romagnolid over 6 years ago
#1008 - RevertSam does not accept /dev/stdin and should have a better error message
Issue -
State: open - Opened by nh13 almost 7 years ago
- 8 comments
Labels: stdin/stdout
#919 - Installation works fine on RHEL6.6 but not Ubuntu 16.04.1 (Xenial Xerus)
Issue -
State: closed - Opened by JonN17 about 7 years ago
#915 - Accept piped input FastqToSam
Issue -
State: closed - Opened by yesimon about 7 years ago
- 7 comments
#831 - Add auxiliary baits and targets to BaitDesigner.
Pull Request -
State: closed - Opened by nh13 over 7 years ago
- 6 comments
#801 - Is it possible to make Picard MarkDuplicates to support multiple threads?
Issue -
State: closed - Opened by liugui over 7 years ago
- 7 comments
#630 - Picard cannot write to stdout
Issue -
State: open - Opened by nh13 about 8 years ago
- 2 comments
Labels: bug, stdin/stdout
#507 - UpdateVcfSequenceDictionary should handle stdin and stdout gracefully
Issue -
State: open - Opened by nh13 over 8 years ago
- 25 comments
Labels: bug, secon, cleanup